RetrogeneDB ID: retro_rnor_1606

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:43634317..43634610(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ska2
• Ensembl ID: ENSRNOG00000025981
• Aliases: Ska2, Fam33a, RGD1307084
• Description: Spindle and kinetochore-associated protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5I0J4]

Sequence

>retro_rnor_1606
GCTGATTTGGATCACATTAGACATAGGCTGGAATACAAAATCAACACCAATCATCCTGATTCAACAGGAGAGAAAAATCC
AATTAAAATCTGAAAGAAATTACCAGCAATGAAGTCTCAATACCAAACTTTGCACACACACTTCAAACCAGTTTCTGTTG
AGCAAAGAGAGATCAAGGGTTGAGTGTGTGCAGTTTTGAGCAGGACGGTGACCCACGTGAGAACAGAGCAGACAGACCTG
GAGCTGACTCTGCTGCCGAAGAGAAAGCCATGACACAACAATCAAAAGCTCAC

Alignment

ORF - retro_rnor_1606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.96 %
• Parental protein coverage: 70.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDLDYLQYRLEYEVKINHPHSAGEKNAVAILKELSAIKSRYQALCARFKTVSVEQKETKSCICAILNKTM
          .DLD....RLEY....NHP.S.GEKN...I.K.L.A.KS.YQ.L...FK.VSVEQ.E.K...CA.L..T.
Retrocopy ADLDHIRHRLEYKINTNHPDSTGEKNPIKI*KKLPAMKSQYQTLHTHFKPVSVEQREIKG*VCAVLSRTV

Parental  TMLQELQKQTNLELTLL-TEEEKAVTERLKSH
          T.......QT.LELTLL..EE.KA.T...K.H
Retrocopy THVR--TEQTDLELTLL<AEE-KAMTQQSKAH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	2.52 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	1.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1606 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606 , retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,